Subgroup Characteristics of Marine Methane-Oxidizing ANME-2 Archaea and Their Syntrophic Partners as Revealed by Integrated Multimodal Analytical Microscopy

ABSTRACTPhylogenetically diverse environmental ANME archaea and sulfate-reducing bacteria cooperatively catalyze the anaerobic oxidation of methane oxidation (AOM) in multicelled consortia within methane seep environments. To better understand these cells and their symbiotic associations, we applied a suite of electron microscopy approaches, including correlative fluorescencein situhybridization-electron microscopy (FISH-EM), transmission electron microscopy (TEM), and serial block face scanning electron microscopy (SBEM) three-dimensional (3D) reconstructions. FISH-EM of methane seep-derived consortia revealed phylogenetic variability in terms of cell morphology, ultrastructure, and storage granules. Representatives of the ANME-2b clade, but not other ANME-2 groups, contained polyphosphate-like granules, while some bacteria associated with ANME-2a/2c contained two distinct phases of iron mineral chains resembling magnetosomes. 3D segmentation of two ANME-2 consortium types revealed cellular volumes of ANME and their symbiotic partners that were larger than previous estimates based on light microscopy. Polyphosphate-like granule-containing ANME (tentatively termed ANME-2b) were larger than both ANME with no granules and partner bacteria. This cell type was observed with up to 4 granules per cell, and the volume of the cell was larger in proportion to the number of granules inside it, but the percentage of the cell occupied by these granules did not vary with granule number. These results illuminate distinctions between ANME-2 archaeal lineages and partnering bacterial populations that are apparently unified in their ability to perform anaerobic methane oxidation.IMPORTANCEMethane oxidation in anaerobic environments can be accomplished by a number of archaeal groups, some of which live in syntrophic relationships with bacteria in structured consortia. Little is known of the distinguishing characteristics of these groups. Here, we applied imaging approaches to better understand the properties of these cells. We found unexpected morphological, structural, and volume variability of these uncultured groups by correlating fluorescence labeling of cells with electron microscopy observables.

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Carbonate-hosted microbial communities are prolific and pervasive methane oxidizers at geologically diverse marine methane seep sites

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2006857118 ◽

2021 ◽

Vol 118 (25) ◽

pp. e2006857118

Author(s):

Jeffrey J. Marlow ◽

Daniel Hoer ◽

Sean P. Jungbluth ◽

Linda M. Reynard ◽

Amy Gartman ◽

...

Keyword(s):

Microbial Communities ◽

Methane Oxidation ◽

Electrical Conductance ◽

Alpha Diversity ◽

Anaerobic Oxidation Of Methane ◽

Methane Seep ◽

Biological Factors ◽

Oxidation Rates ◽

Continental Scale ◽

Oxidation Of Methane

At marine methane seeps, vast quantities of methane move through the shallow subseafloor, where it is largely consumed by microbial communities. This process plays an important role in global methane dynamics, but we have yet to identify all of the methane sinks in the deep sea. Here, we conducted a continental-scale survey of seven geologically diverse seafloor seeps and found that carbonate rocks from all sites host methane-oxidizing microbial communities with substantial methanotrophic potential. In laboratory-based mesocosm incubations, chimney-like carbonates from the newly described Point Dume seep off the coast of Southern California exhibited the highest rates of anaerobic methane oxidation measured to date. After a thorough analysis of physicochemical, electrical, and biological factors, we attribute this substantial metabolic activity largely to higher cell density, mineral composition, kinetic parameters including an elevated Vmax, and the presence of specific microbial lineages. Our data also suggest that other features, such as electrical conductance, rock particle size, and microbial community alpha diversity, may influence a sample’s methanotrophic potential, but these factors did not demonstrate clear patterns with respect to methane oxidation rates. Based on the apparent pervasiveness within seep carbonates of microbial communities capable of performing anaerobic oxidation of methane, as well as the frequent occurrence of carbonates at seeps, we suggest that rock-hosted methanotrophy may be an important contributor to marine methane consumption.

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Microbial Diversity of Hydrothermal Sediments in the Guaymas Basin: Evidence for Anaerobic Methanotrophic Communities

Applied and Environmental Microbiology ◽

10.1128/aem.68.4.1994-2007.2002 ◽

2002 ◽

Vol 68 (4) ◽

pp. 1994-2007 ◽

Cited By ~ 484

Author(s):

Andreas Teske ◽

Kai-Uwe Hinrichs ◽

Virginia Edgcomb ◽

Alvin de Vera Gomez ◽

David Kysela ◽

...

Keyword(s):

16S Rrna ◽

Methane Oxidation ◽

Gulf Of California ◽

Trophic Ecology ◽

Anaerobic Methane Oxidation ◽

Anaerobic Oxidation Of Methane ◽

Anaerobic Oxidation ◽

Bacterial Populations ◽

Guaymas Basin ◽

Oxidation Of Methane

ABSTRACT Microbial communities in hydrothermally active sediments of the Guaymas Basin (Gulf of California, Mexico) were studied by using 16S rRNA sequencing and carbon isotopic analysis of archaeal and bacterial lipids. The Guaymas sediments harbored uncultured euryarchaeota of two distinct phylogenetic lineages within the anaerobic methane oxidation 1 (ANME-1) group, ANME-1a and ANME-1b, and of the ANME-2c lineage within the Methanosarcinales, both previously assigned to the methanotrophic archaea. The archaeal lipids in the Guaymas Basin sediments included archaeol, diagnostic for nonthermophilic euryarchaeota, and sn-2-hydroxyarchaeol, with the latter compound being particularly abundant in cultured members of the Methanosarcinales. The concentrations of these compounds were among the highest observed so far in studies of methane seep environments. The δ-13C values of these lipids (δ-13C = −89 to −58‰) indicate an origin from anaerobic methanotrophic archaea. This molecular-isotopic signature was found not only in samples that yielded predominantly ANME-2 clones but also in samples that yielded exclusively ANME-1 clones. ANME-1 archaea therefore remain strong candidates for mediation of the anaerobic oxidation of methane. Based on 16S rRNA data, the Guaymas sediments harbor phylogenetically diverse bacterial populations, which show considerable overlap with bacterial populations of geothermal habitats and natural or anthropogenic hydrocarbon-rich sites. Consistent with earlier observations, our combined evidence from bacterial phylogeny and molecular-isotopic data indicates an important role of some novel deeply branching bacteria in anaerobic methanotrophy. Anaerobic methane oxidation likely represents a significant and widely occurring process in the trophic ecology of methane-rich hydrothermal vents. This study stresses a high diversity among communities capable of anaerobic oxidation of methane.

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Anaerobic oxidation of methane in grassland soils used for cattle husbandry

Biogeosciences ◽

10.5194/bg-9-3891-2012 ◽

2012 ◽

Vol 9 (10) ◽

pp. 3891-3899 ◽

Cited By ~ 10

Author(s):

A. Bannert ◽

C. Bogen ◽

J. Esperschütz ◽

A. Koubová ◽

F. Buegger ◽

...

Keyword(s):

Methane Oxidation ◽

Enrichment Culture ◽

Anaerobic Oxidation Of Methane ◽

Anaerobic Oxidation ◽

Incubation Experiment ◽

Nutrient Source ◽

Oxidation Activity ◽

Oxidation Of Methane ◽

Cattle Husbandry

Abstract. While the importance of anaerobic methane oxidation has been reported for marine ecosystems, the role of this process in soils is still questionable. Grasslands used as pastures for cattle overwintering show an increase in anaerobic soil micro-sites caused by animal treading and excrement deposition. Therefore, anaerobic potential methane oxidation activity of severely impacted soil from a cattle winter pasture was investigated in an incubation experiment under anaerobic conditions using 13C-labelled methane. We were able to detect a high microbial activity utilizing CH4 as nutrient source shown by the respiration of 13CO2. Measurements of possible terminal electron acceptors for anaerobic oxidation of methane were carried out. Soil sulfate concentrations were too low to explain the oxidation of the amount of methane added, but enough nitrate and iron(III) were detected. However, only nitrate was consumed during the experiment. 13C-PLFA analyses clearly showed the utilization of CH4 as nutrient source mainly by organisms harbouring 16:1ω7 PLFAs. These lipids were also found as most 13C-enriched fatty acids by Raghoebarsing et al. (2006) after addition of 13CH4 to an enrichment culture coupling denitrification of nitrate to anaerobic oxidation of methane. This might be an indication for anaerobic oxidation of methane by relatives of "Candidatus Methylomirabilis oxyfera" in the investigated grassland soil under the conditions of the incubation experiment.

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Anaerobic Oxidation of Methane in Sediments of Lake Constance, an Oligotrophic Freshwater Lake

Applied and Environmental Microbiology ◽

10.1128/aem.00340-11 ◽

2011 ◽

Vol 77 (13) ◽

pp. 4429-4436 ◽

Cited By ~ 141

Author(s):

Jörg S. Deutzmann ◽

Bernhard Schink

Keyword(s):

Methane Oxidation ◽

Electron Acceptors ◽

Molecular Techniques ◽

Freshwater Lake ◽

Lake Constance ◽

Anaerobic Oxidation Of Methane ◽

Anaerobic Oxidation ◽

Terminal Electron Acceptor ◽

Oxidation Of Methane ◽

Freshwater Habitats

ABSTRACTAnaerobic oxidation of methane (AOM) with sulfate as terminal electron acceptor has been reported for various environments, including freshwater habitats, and also, nitrate and nitrite were recently shown to act as electron acceptors for methane oxidation in eutrophic freshwater habitats. Radiotracer experiments with sediment material of Lake Constance, an oligotrophic freshwater lake, were performed to follow14CO2formation from14CH4in sediment incubations in the presence of different electron acceptors, namely, nitrate, nitrite, sulfate, or oxygen. Whereas14CO2formation without and with sulfate addition was negligible, addition of nitrate increased14CO2formation significantly, suggesting that AOM could be coupled to denitrification. Nonetheless, denitrification-dependent AOM rates remained at least 1 order of magnitude lower than rates of aerobic methane oxidation. Using molecular techniques, putative denitrifying methanotrophs belonging to the NC10 phylum were detected on the basis of thepmoAand 16S rRNA gene sequences. These findings show that sulfate-dependent AOM was insignificant in Lake constant sediments. However, AOM can also be coupled to denitrification in this oligotrophic freshwater habitat, providing first indications that this might be a widespread process that plays an important role in mitigating methane emissions.

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Comparative Analysis of Methane-Oxidizing Archaea and Sulfate-Reducing Bacteria in Anoxic Marine Sediments

Applied and Environmental Microbiology ◽

10.1128/aem.67.4.1922-1934.2001 ◽

2001 ◽

Vol 67 (4) ◽

pp. 1922-1934 ◽

Cited By ~ 454

Author(s):

V. J. Orphan ◽

K.-U. Hinrichs ◽

W. Ussler ◽

C. K. Paull ◽

L. T. Taylor ◽

...

Keyword(s):

Marine Sediments ◽

Sulfate Reducing Bacteria ◽

Rrna Gene ◽

Anaerobic Oxidation Of Methane ◽

Ether Lipids ◽

Methane Seep ◽

Sulfate Reducing ◽

Oxidation Of Methane ◽

Close Relatives ◽

Reducing Bacteria

ABSTRACT The oxidation of methane in anoxic marine sediments is thought to be mediated by a consortium of methane-consuming archaea and sulfate-reducing bacteria. In this study, we compared results of rRNA gene (rDNA) surveys and lipid analyses of archaea and bacteria associated with methane seep sediments from several different sites on the Californian continental margin. Two distinct archaeal lineages (ANME-1 and ANME-2), peripherally related to the orderMethanosarcinales, were consistently associated with methane seep marine sediments. The same sediments contained abundant13C-depleted archaeal lipids, indicating that one or both of these archaeal groups are members of anaerobic methane-oxidizing consortia. 13C-depleted lipids and the signature 16S rDNAs for these archaeal groups were absent in nearby control sediments. Concurrent surveys of bacterial rDNAs revealed a predominance of δ-proteobacteria, in particular, close relatives ofDesulfosarcina variabilis. Biomarker analyses of the same sediments showed bacterial fatty acids with strong 13C depletion that are likely products of these sulfate-reducing bacteria. Consistent with these observations, whole-cell fluorescent in situ hybridization revealed aggregations of ANME-2 archaea and sulfate-reducing Desulfosarcina andDesulfococcus species. Additionally, the presence of abundant 13C-depleted ether lipids, presumed to be of bacterial origin but unrelated to ether lipids of members of the orderDesulfosarcinales, suggests the participation of additional bacterial groups in the methane-oxidizing process. Although theDesulfosarcinales and ANME-2 consortia appear to participate in the anaerobic oxidation of methane in marine sediments, our data suggest that other bacteria and archaea are also involved in methane oxidation in these environments.

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Anaerobic oxidation of methane in grassland soils used for cattle husbandry

Biogeosciences Discussions ◽

10.5194/bgd-9-4919-2012 ◽

2012 ◽

Vol 9 (4) ◽

pp. 4919-4945

Author(s):

A. Bannert ◽

C. Bogen ◽

J. Esperschütz ◽

A. Koubová ◽

F. Buegger ◽

...

Keyword(s):

Methane Oxidation ◽

Anaerobic Methane Oxidation ◽

Anaerobic Oxidation Of Methane ◽

Type I ◽

Anaerobic Oxidation ◽

Nutrient Source ◽

Oxidation Activity ◽

Oxidation Of Methane ◽

Cattle Husbandry

Abstract. While the importance of anaerobic methane oxidation has been reported for marine ecosystems, the role of this process in soils is still questionable. Grasslands used as pastures for cattle-overwintering show an increase in anaerobic soil micro-sites caused by animal treading and excrement deposition. Therefore anaerobic potential methane oxidation activity of severely impacted soil from a cattle winter pasture was investigated in an incubation experiment under anaerobic conditions using 13C-labeled methane. We were able to detect a high microbial activity utilizing CH4 as nutrient source shown by the respiration of 13CO2. Measurements of possible terminal electron acceptors for anaerobic oxidation of methane were carried out. Soil sulfate concentrations were too low to explain the oxidation of the amount of methane added, but enough nitrate and iron(III) were detected. However, only nitrate was consumed during the experiment. 13C-PLFA analyses clearly showed the utilization of CH4 as nutrient source mainly by organisms harbouring 16:1ω7 PLFAs. These lipids were found in Gram-negative microorganisms and anaerobes. The fact that these lipids are also typical for type I methanotrophs, known as aerobic methane oxidizers, might indicate a link between aerobic and anaerobic methane oxidation.

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Modification of methane oxidation pathways during long-term incubations of methanic lake sediments

10.5194/bg-2021-223 ◽

2021 ◽

Author(s):

Hanni Vigderovich ◽

Werner Eckert ◽

Michal Elul ◽

Maxim Rubin-Blum ◽

Marcus Elvert ◽

...

Keyword(s):

Lake Sediments ◽

Carbon Isotope ◽

Iron Oxides ◽

Methane Oxidation ◽

Electron Acceptors ◽

Anaerobic Oxidation Of Methane ◽

Methanotrophic Bacteria ◽

Oxidation Of Methane ◽

Isotope Measurements

Abstract. Anaerobic oxidation of methane (AOM) is one of the major processes limiting the release of the greenhouse gas methane from natural environments. In Lake Kinneret sediments, iron-coupled AOM (Fe-AOM) was suggested to play a substantial role (10–15 % relative to methanogenesis) in the methanic zone (> 20 cm sediment depth), based on geochemical profiles and experiments on fresh sediments. Apparently, the oxidation of methane is mediated by a combination of mcr gene bearing archaea and aerobic bacterial methanotrophs. Here we aimed to investigate the survival of this complex microbial interplay under controlled conditions. We followed the AOM process during long-term (~18 months) anaerobic slurry experiments of these methanic sediments with two stages of incubations and additions of 13C-labeled methane, multiple electron acceptors and inhibitors. After these incubation stages carbon isotope measurements in the dissolved inorganic pool still showed considerable AOM (3–8 % relative to methanogenesis). Specific lipid carbon isotope measurements and metagenomic analyses indicate that after the prolonged incubation aerobic methanotrophic bacteria were no longer involved in the oxidation process, whereas mcr gene bearing archaea were most likely responsible for oxidizing the methane. Humic substances and iron oxides are likely electron acceptors to support this oxidation, whereas sulfate, manganese, nitrate, and nitrite did not support the AOM in these methanic sediments. Our results suggest in the natural lake sediments methanotrophic bacteria are responsible for part of the methane oxidation by the reduction of combined micro levels of oxygen and iron oxides in a cryptic cycle, while the rest of the methane is converted by reverse methanogenesis. After long-term incubation, the latter prevails without bacterial methanotropic activity and with a different iron reduction pathway.

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Anaerobic Oxidation of Methane Coupled to Nitrite Reduction by Halophilic Marine NC10 Bacteria

Applied and Environmental Microbiology ◽

10.1128/aem.00984-15 ◽

2015 ◽

Vol 81 (16) ◽

pp. 5538-5545 ◽

Cited By ~ 42

Author(s):

Zhanfei He ◽

Sha Geng ◽

Chaoyang Cai ◽

Shuai Liu ◽

Yan Liu ◽

...

Keyword(s):

16S Rrna ◽

Methane Oxidation ◽

Nitrite Reduction ◽

Substrate Affinity ◽

Rrna Gene ◽

Anaerobic Oxidation Of Methane ◽

Anaerobic Oxidation ◽

Oxidation Activity ◽

Optimal Salinity ◽

Oxidation Of Methane

ABSTRACTAnaerobic oxidation of methane (AOM) coupled to nitrite reduction is a novel AOM process that is mediated by denitrifying methanotrophs. To date, enrichments of these denitrifying methanotrophs have been confined to freshwater systems; however, the recent findings of 16S rRNA andpmoAgene sequences in marine sediments suggest a possible occurrence of AOM coupled to nitrite reduction in marine systems. In this research, a marine denitrifying methanotrophic culture was obtained after 20 months of enrichment. Activity testing and quantitative PCR (qPCR) analysis were then conducted and showed that the methane oxidation activity and the number of NC10 bacteria increased correlatively during the enrichment period. 16S rRNA gene sequencing indicated that only bacteria in group A of the NC10 phylum were enriched and responsible for the resulting methane oxidation activity, although a diverse community of NC10 bacteria was harbored in the inoculum. Fluorescencein situhybridization showed that NC10 bacteria were dominant in the enrichment culture after 20 months. The effect of salinity on the marine denitrifying methanotrophic culture was investigated, and the apparent optimal salinity was 20.5‰, which suggested that halophilic bacterial AOM coupled to nitrite reduction was obtained. Moreover, the apparent substrate affinity coefficients of the halophilic denitrifying methanotrophs were determined to be 9.8 ± 2.2 μM for methane and 8.7 ± 1.5 μM for nitrite.

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Clumped Isotopologue Fractionation by Microbial Cultures Performing the Anaerobic 10 Oxidation of Methane

10.26434/chemrxiv.12888347.v1 ◽

2020 ◽

Author(s):

Shuhei Ono ◽

Jeemin H. Rhim ◽

Danielle S. Gruen ◽

Heidi Taubner ◽

Martin Kölling ◽

...

Keyword(s):

Methane Oxidation ◽

Marine Sediments ◽

Anaerobic Oxidation Of Methane ◽

Sources And Sinks ◽

Oxidation Of Methane ◽

Microbial Cultures ◽

Relative Composition ◽

Subsurface Sediments ◽

Stochastic Distribution ◽

Methane Sink

Methane is abundant in marine subsurface sediments, sourced from microbial or thermocatalytic products. The relative composition of its isotopologues (12CH4, 13CH4, 12CH3D and 13CH3D) is used to infer its sources and sinks. The anaerobic oxidation of methane (AOM) is an important methane sink reaction carried out by consortia of<br>anaerobic methanotrophic archaea (ANME) and partner bacteria in the presence of methane and sulfate. We investigated the methane isotopologue fractionations during<br>AOM in experiments with cultures of ANME-1 archaea and partner bacteria obtained from hydrothermally heated gas-rich sediments of the Guaymas Basin. During partial methane consumption in four sets of experiments, residual methane became enriched in 13CH4 and 12CH3D, following kinetic fractionations from 11.1 to 18.3 ‰ and from 117 to 180 ‰,respectively. Results from one set of experiments with D-depleted medium water (δD = – 200‰, whereas the control was –55‰) are inconclusive regarding the reversibility of AOM, which would lead to equilibrium as opposed to kinetic fractionations. The value of Δ13CH3D (the abundance of 13CH3D with respect to that expected from stochastic distribution) increased toward and beyond (up to 8.4‰) the value expected for isotopologue equilibrium (5.3‰ at 37 °C). The kinetic clumped isotopologue fractionation (difference between 13CH3D/12CH3D and 13CH4/12CH4 fractionations) of 4.8 to 12.8 ‰ is in contrast with our previous observation of little to no clumped isotopologue effect during aerobic methane oxidation. Our results demonstrate that AOM can contribute to near52<br>equilibrium Δ13CH3D values observed in marine sediments and 13CH3D systematics can be used to distinguish aerobic versus anaerobic methanotrophic processes in nature.

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Diversity and Metabolic Potential of the Terrestrial Mud Volcano Microbial Community with a High Abundance of Archaea Mediating the Anaerobic Oxidation of Methane

Life ◽

10.3390/life11090953 ◽

2021 ◽

Vol 11 (9) ◽

pp. 953

Author(s):

Alexander Y. Merkel ◽

Nikolay A. Chernyh ◽

Nikolai V. Pimenov ◽

Elizaveta A. Bonch-Osmolovskaya ◽

Alexander I. Slobodkin

Keyword(s):

Methane Oxidation ◽

Current Knowledge ◽

High Abundance ◽

Rrna Gene ◽

Anaerobic Oxidation Of Methane ◽

Community Members ◽

Metabolic Potential ◽

Oxidation Of Methane ◽

Complete Set ◽

Phylogenetic Composition

Terrestrial mud volcanoes (TMVs) are important natural sources of methane emission. The microorganisms inhabiting these environments remain largely unknown. We studied the phylogenetic composition and metabolic potential of the prokaryotic communities of TMVs located in the Taman Peninsula, Russia, using a metagenomic approach. One of the examined sites harbored a unique community with a high abundance of anaerobic methane-oxidizing archaea belonging to ANME-3 group (39% of all 16S rRNA gene reads). The high number of ANME-3 archaea was confirmed by qPCR, while the process of anaerobic methane oxidation was demonstrated by radioisotopic experiments. We recovered metagenome-assembled genomes (MAGs) of archaeal and bacterial community members and analyzed their metabolic capabilities. The ANME-3 MAG contained a complete set of genes for methanogenesis as well as of ribosomal RNA and did not encode proteins involved in dissimilatory nitrate or sulfate reduction. The presence of multiheme c-type cytochromes suggests that ANME-3 can couple methane oxidation with the reduction of metal oxides or with the interspecies electron transfer to a bacterial partner. The bacterial members of the community were mainly represented by autotrophic, nitrate-reducing, sulfur-oxidizing bacteria, as well as by fermentative microorganisms. This study extends the current knowledge of the phylogenetic and metabolic diversity of prokaryotes in TMVs and provides a first insight into the genomic features of ANME-3 archaea.

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